GATK Best practices for variant discovery

Trainer Geraldine Van der Auwera
BITS Courses TRAINING AT VIB

Goal

This workshop will focus on the core steps involved in calling variants with the BroadÔÇÖs Genome Analysis Toolkit, using the ÔÇ£Best PracticesÔÇØ developed by the GATK team. You will learn 

  • why each step is essential to the variant discovery process
  • what are the operations performed on the data at each step
  • how to use the GATK tools to get the most accurate and reliable results out of your dataset.

Summary

ÔÇïIn the course of this workshop, we highlight key functionalities such as 

  • GVCF workflow for joint variant discovery in cohorts
  • RNAseq-specific processing
  • somatic variant discovery using MuTect2. 
  • capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery
  • the use of pipelining tools to assemble and execute GATK workflows.

Prerequisites

Familiarity with
ÔùÅ    NGS data formats: FASTQ, SAM/BAM, VCF
ÔùÅ    the use of Linux command line
People who lack these skills can follow the 'Prep course for GATKÔÇï' on 10 February.
Supported operating systems: MacOSX or Linux. Microsoft Windows is NOT supported.

Schedule

See the TRAINING AT VIB website for a detailed schedule of this training.

Training material

Links

None

Scientific topics RNA-Seq, DNA mapping
Target audience Life Science Researchers, PhD students, post-docs, beginner bioinformaticians